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9pmc

The 100-K crystal structure of CYP199A4 bound to 3-methylaminobenzoic acid (dataset 3; decreasing temperature series)

Method: X-RAY DIFFRACTION D_max: 66.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pmc
deposition_date	2025-07-17
title	The 100-K crystal structure of CYP199A4 bound to 3-methylaminobenzoic acid (dataset 3; decreasing temperature series)
keywords	Cytochrome P450, variable-temperature crystallography, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	21.45 Å
rg_electron	20.31 Å
i0	32061700.00
molecular_weight	43645.0 kDa
excluded_volume	54636 Å³
envelope_volume	60767 Å³
shell_volume	24336 Å³
envelope_diameter	68.6 Å
shell_rg	27.41 Å
envelope_rg	20.51 Å
shape_rg	20.29 Å
total_rg	21.24 Å
total_atoms	3076
n_residues	393
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	66.5 Å
rg_real	21.30 Å
rg_real_error	0.29 Å
i0_real	3.2060e+07
i0_real_error	3.9910e+05
rg_reciprocal	21.33 Å
i0_reciprocal	32060000.0000
total_estimate	0.9019
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	27.4 Å
skewness	0.135
kurtosis	-0.485
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	7034000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Cytochrome P450
formula_weight	44587.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3629

MISNSSAESISAPPNDSTIPHLAIDPFSLDFFDDPYPDQQTLRDAGPVVYLDKWNVYGVARYAEVHAVLNDPTTFCSSRGVGLSDFKKEKPWRPPSLILEADPPAHTRPRAVLSKVLSPATMKTIRDGFAAAADAKVDELLQRGCIDAIADLAEAYPLSVFPDAMGLKQEGREHLLPYAGLVFNAFGPPNELRQTAIERSAPHQAYVNEQCQRPNLAPGGFGACIHAFTDTGEITPDEAPLLVRSLLSAGLDTTVNGIGAAVYCLARFPGELQRLRSDPTLARNAFEEAVRFESPVQTFFRTTTREVELGGAVIGEGEKVLMFLGSANRDPRRWSDPDLYDITRKTSGHVGFGSGVHMCVGQLVARLEGEVMLSALARKVAAIDIDGPVKRRFNNTLRGLESLPVKLTPA

Source

organism	Rhodopseudomonas palustris HaA2
ncbi_taxonomy_id	316058
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	3-(methylamino)benzoic acid
formula_weight	151.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	471

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6. Citations (1)

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length_a	44.177 Å
length_b	51.365 Å
length_c	78.983 Å
angle_alpha	90.00 °
angle_beta	92.16 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.507 Å
resolution_low	44.145 Å
r_factor	0.1715
r_work	0.1703
r_free	0.2063

fit	/app/data/saxs_computation/pm/9pmc/9pmc.fit
pddf	/app/data/pr_computation/pm/9pmc/9pmc.pr.out
profile	/app/data/saxs_computation/pm/9pmc/9pmc.dat